Installation on Apple M1

sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

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Installation on Apple M1 #247

Open sneumann opened 3 years ago

sneumann commented 3 years ago

Hi @Steffen Neumann -- I tried to install mzR (2.26.0) with BiocManager (for bioc 3.13, release) on >M1 mac but hit an error because boost/smart_ptr/detail/atomic_count_sync.hpp is not present in the >mzR source (master or RELEASE_3_13). I copied the file over from BH and was able to install from source. This is just FYI.

Thanks @vjcitn for reporting!

Yours, Steffen

sneumann commented 2 years ago

Hi @vjcitn , does mzR >= 2.29.3 work now on M1 ? If yes, please report back so we can close this issue. Yours, Steffen

vjcitn commented 2 years ago

not sure

Loading required package: Rcpp
Error in dyn.load(dll_copy_file) : 
  unable to load shared object '/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T//RtmpaDXbss/pkgload167007e703e20/mzR.so':
  dlopen(/var/folders/n4/p9th81md60s8nv12yv40sv8m0000gp/T//RtmpaDXbss/pkgload167007e703e20/mzR.so, 0x0006): symbol not found in flat namespace '_mzR_pwiz_version'
Calls: <Anonymous> ... <Anonymous> -> load_dll -> library.dynam2 -> dyn.load

can't say my system is well-configured so maybe there are solutions to be found. hope to be able to provide more data in a few days.

sneumann commented 2 years ago

At least it is a different error :-) Seems to do with Rcpp now. Should be in RcppExports:

for F in $(find . -name "*.o") ; do echo $F ; nm $F | c++filt  | grep pwiz_version ; done
./RcppExports.o
0000000000000000 T mzR_pwiz_version

Although, your message has an extra _ in the symbol name. Yours, Steffen